Modeling the Breakage-Fusion-Bridge Mechanism: Combinatorics and Cancer Genomics

  • Marcus Kinsella
  • Vineet Bafna
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7262)


The breakage-fusion-bridge (BFB) mechanism was proposed over seven decades ago and is a source of genomic variability and gene amplification in cancer. Here we formally model and analyze the BFB mechanism, to our knowledge this first time this has been undertaken. We show that BFB can be modeled as successive inverted prefix duplications of a string. Using this model, we show that BFB can achieve a surprisingly broad range of amplification patterns. We find that a sequence of BFB operations can be found that nearly fits most patterns of copy number increases along a chromosome. We conclude that this limits the usefulness of methods like array CGH for detecting BFB and discuss other implications for understanding mechanisms of genomic instability.


cancer genomics algorithms combinatorial pattern matching gene amplification 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Marcus Kinsella
    • 1
  • Vineet Bafna
    • 2
  1. 1.Bioinformatics and Systems Biology ProgramUniversity of CaliforniaSan DiegoUSA
  2. 2.Department of Computer Science and EngineeringUniversity of CaliforniaSan DiegoUSA

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